Fig. 2: Microbiota variation across device types suggests patchy structure.

a, Microbiota composition varied significantly more between intestinal samples than between stool samples (P = 1.5 × 10⁻⁷ within participants and P = 2.3 × 10⁻²² across participants) or between saliva samples (P = 1.5 × 10⁻⁷ within participants and P = 3.5 × 10⁻³⁵ across participants). Top, each point is the mean pairwise Canberra distance between all samples for a participant (n = 14, 15 and 14 for stool, devices and saliva, respectively). Bottom, each point is the mean of all pairwise comparisons between all samples from any two participants (n = 105, 105 and 105 for stool, devices and saliva, respectively). b, Combinations of spatial, temporal and technical (n = 15 each) variability in the microbiota composition of intestinal samples (gray) were higher than in technical replicates (n = 8; light brown) in which one participant swallowed four of the same device type simultaneously (the participant did so twice for each of the four device types). Each point represents the mean pairwise Canberra distance between intestinal samples from the same participant. Microbial communities from devices of the same type ingested at the same time were more similar than those from devices of the same type ingested at different times, although this difference was not statistically robust (P = 0.058) given the small number of observations. c, Devices were more likely to be dominated by a single ASV as compared with stool or saliva. Each point is a single sample (n = 29 for saliva, n = 56, 54, 55 and 45 for device types 1–4, respectively, and n = 58 for stool). d, The Shannon diversity of saliva and stool samples was higher than that of intestinal samples (saliva to device type 1, P = 5.3 × 10⁻⁷; device type 4 to stool, P = 2.9 × 10⁻⁹). Each point is a single sample (n = 29 for saliva, n = 56, 54, 55 and 45 for device types 1–4, respectively, and n = 58 for stool). Boxplots show the median value and the first and third quartiles. *P ≤ 0.05, ****P ≤ 0.0001, Bonferroni-adjusted two-sided Wilcoxon rank-sum test. Canberra distances for a,b were computed from log₂-transformed read counts of 16S rRNA gene ASVs with read count ≥3 in ≥5% of samples (including all repeatability samples) (n = 446).